Merge branch 'remark' of gitlab.it4i.cz:it4i-admins/docs.it4i into remark

docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-ddt.md

@@ -47,9 +47,8 @@ $ mpif90 -g -O0 -o test_debug test.f
 
 Before debugging, you need to compile your code with theses flags:
 
-!!! Note "Note"
-	\- **g** : Generates extra debugging information usable by GDB. -g3 includes even more debugging information. This option is available for GNU and INTEL C/C++ and Fortran compilers.
-
+!!! Note
+    - **g** : Generates extra debugging information usable by GDB. -g3 includes even more debugging information. This option is available for GNU and INTEL C/C++ and Fortran compilers.
     - **O0** : Suppress all optimizations.
 
 ## Starting a Job with DDT

docs.it4i/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md

 # Allinea Performance Reports
 
-\##quick application profiling
-
 ## Introduction
 
 Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs.
@@ -31,7 +29,7 @@ Instead of [running your MPI program the usual way](../mpi/), use the the perf r
     $ perf-report mpirun ./mympiprog.x
 ```
 
-The mpi program will run as usual. The perf-report creates two additional files, in _.txt and _.html format, containing the performance report. Note that [demanding MPI codes should be run within the queue system](../../resource-allocation-and-job-execution/job-submission-and-execution/).
+The mpi program will run as usual. The perf-report creates two additional files, in \*.txt and \*.html format, containing the performance report. Note that [demanding MPI codes should be run within the queue system](../../resource-allocation-and-job-execution/job-submission-and-execution/).
 
 ## Example
 

docs.it4i/salomon/environment-and-modules.md

@@ -26,9 +26,6 @@ fi
 !!! Note "Note"
 	Do not run commands outputting to standard output (echo, module list, etc) in .bashrc  for non-interactive SSH sessions. It breaks fundamental functionality (scp, PBS) of your account! Take care for SSH session interactivity for such commands as stated in the previous example.
 
-How to using modules in examples:
-<tty-player controls src=/src/salomon/modules_salomon.ttyrec></tty-player>
-
 ### Application Modules
 
 In order to configure your shell for  running particular application on Salomon we use Module package interface.

docs.it4i/salomon/ib-single-plane-topology.md

@@ -8,7 +8,7 @@ The SGI ICE X IB Premium Blade provides the first level of interconnection via d
 -   3 ports on each chip provide connectivity between the chips
 -   24 ports from each switch chip connect to the external bulkhead, for a total of 48
 
-\###IB single-plane topology - ICEX M-Cell
+### IB single-plane topology - ICEX M-Cell
 
 Each color in each physical IRU represents one dual-switch ASIC switch.
 

docs.it4i/salomon/job-priority.md

@@ -29,8 +29,8 @@ Fair-share priority is calculated as
 ![](../img/fairshare_formula.png)
 
 where MAX_FAIRSHARE has value 1E6,
-usage_Project_ is cumulated usage by all members of selected project,
-usage_Total_ is total usage by all users, by all projects.
+usage<sub>Project</sub> is cumulated usage by all members of selected project,
+usage<sub>Total</sub> is total usage by all users, by all projects.
 
 Usage counts allocated core-hours (`ncpus x walltime`). Usage is decayed, or cut in half periodically, at the interval 168 hours (one week).
 
@@ -41,7 +41,7 @@ Usage counts allocated core-hours (`ncpus x walltime`). Usage is decayed, or cut
 
 Calculated fair-share priority can be also seen as Resource_List.fairshare attribute of a job.
 
-\###Eligible time
+### Eligible time
 
 Eligible time is amount (in seconds) of eligible time job accrued while waiting to run. Jobs with higher eligible time gains higher priority.
 

docs.it4i/salomon/job-submission-and-execution.md

@@ -257,7 +257,7 @@ Job ID          Username Queue    Jobname    SessID NDS TSK Memory Time  S Time
 16547.isrv5     user2    qprod    job3x       13516   2  32    --  48:00 R 00:58
 ```
 
-In this example user1 and user2 are running jobs named job1, job2 and job3x. The jobs job1 and job2 are using 4 nodes, 16 cores per node each. The job1 already runs for 38 hours and 25 minutes, job2 for 17 hours 44 minutes. The job1 already consumed 64_38.41 = 2458.6 core hours. The job3x already consumed 0.96_32 = 30.93 core hours. These consumed core hours will be accounted on the respective project accounts, regardless of whether the allocated cores were actually used for computations.
+In this example user1 and user2 are running jobs named job1, job2 and job3x. The jobs job1 and job2 are using 4 nodes, 16 cores per node each. The job1 already runs for 38 hours and 25 minutes, job2 for 17 hours 44 minutes. The job1 already consumed 64 x 38.41 = 2458.6 core hours. The job3x already consumed 0.96 x 32 = 30.93 core hours. These consumed core hours will be accounted on the respective project accounts, regardless of whether the allocated cores were actually used for computations.
 
 Check status of your jobs using check-pbs-jobs command. Check presence of user's PBS jobs' processes on execution hosts. Display load, processes. Display job standard and error output. Continuously display (tail -f) job standard or error output.
 

docs.it4i/salomon/software/debuggers/allinea-performance-reports.md

@@ -28,7 +28,7 @@ Instead of [running your MPI program the usual way](../mpi/mpi/), use the the pe
     $ perf-report mpirun ./mympiprog.x
 ```
 
-The mpi program will run as usual. The perf-report creates two additional files, in _.txt and _.html format, containing the performance report. Note that  demanding MPI codes should be run within [ the queue system](../../resource-allocation-and-job-execution/job-submission-and-execution/).
+The mpi program will run as usual. The perf-report creates two additional files, in \*.txt and \*.html format, containing the performance report. Note that  demanding MPI codes should be run within [ the queue system](../../resource-allocation-and-job-execution/job-submission-and-execution/).
 
 ## Example
 

docs.it4i/salomon/software/debuggers/intel-vtune-amplifier.md

@@ -2,7 +2,7 @@
 
 ## Introduction
 
-Intel_® _VTune™ Amplifier, part of Intel Parallel studio, is a GUI profiling tool designed for Intel processors. It offers a graphical performance analysis of single core and multithreaded applications. A highlight of the features:
+Intel *®* VTune™ Amplifier, part of Intel Parallel studio, is a GUI profiling tool designed for Intel processors. It offers a graphical performance analysis of single core and multithreaded applications. A highlight of the features:
 
 -   Hotspot analysis
 -   Locks and waits analysis
@@ -62,11 +62,11 @@ It is possible to analyze both native and offloaded Xeon Phi applications.
 
 ### Native mode
 
-This mode is useful for native Xeon Phi applications launched directly on the card. In _Analysis Target_ window, select _Intel Xeon Phi coprocessor (native), _choose path to the binary and MIC card to run on.
+This mode is useful for native Xeon Phi applications launched directly on the card. In *Analysis Target* window, select *Intel Xeon Phi coprocessor (native)*, choose path to the binary and MIC card to run on.
 
 ### Offload mode
 
-This mode is useful for applications that are launched from the host and use offload, OpenCL or mpirun. In _Analysis Target_ window, select _Intel Xeon Phi coprocessor (native), _choose path to the binaryand MIC card to run on.
+This mode is useful for applications that are launched from the host and use offload, OpenCL or mpirun. In *Analysis Target* window, select *Intel Xeon Phi coprocessor (native)*, choose path to the binaryand MIC card to run on.
 
 !!! Note "Note"
 	If the analysis is interrupted or aborted, further analysis on the card might be impossible and you will get errors like "ERROR connecting to MIC card". In this case please contact our support to reboot the MIC card.
@@ -89,6 +89,6 @@ You can obtain this command line by pressing the "Command line..." button on Ana
 
 ## References
 
-1.  <https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf> Performance Tuning for Intel® Xeon Phi™ Coprocessors
-2.  <https://software.intel.com/en-us/intel-vtune-amplifier-xe-support/documentation> >Intel® VTune™ Amplifier Support
-3.  <https://software.intel.com/en-us/amplifier_help_linux>
+1. [Performance Tuning for Intel® Xeon Phi™ Coprocessors](https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf)
+2. [Intel® VTune™ Amplifier Support](https://software.intel.com/en-us/intel-vtune-amplifier-xe-support/documentation)
+3. [https://software.intel.com/en-us/amplifier_help_linux](https://software.intel.com/en-us/amplifier_help_linux)